ArticleRNA (New York, N.Y.)2010
Predicting in vivo binding sites of RNA-binding proteins using mRNA secondary structure.
Article in RNA (New York, N.Y.), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 115 papers, 1 of them a synthesis that pooled it.
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Who cites it
115 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A Systematic Review and Meta-Analysis for the Association of Gene Polymorphisms in RAN with Cancer Risk.Disease markers · 2020Pooled it
- A resource of RNA-binding protein motifs across eukaryotes reveals evolutionary dynamics and gene-regulatory function.Nature biotechnology · 2026Article
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- Evaluation of novel computational methods to identify RNA-binding protein footprints from structural data.RNA (New York, N.Y.) · 2025Article
- Dissecting RNA selectivity mediated by tandem RNA-binding domains.The Journal of biological chemistry · 2025Article
- Molecular targets and strategies in the development of nucleic acid cancer vaccines: from shared to personalized antigens.Journal of biomedical science · 2024Review
- Pumilio-1 mediated translational control of claudin-5 at the blood-brain barrier.Fluids and barriers of the CNS · 2024Article
- Regulation by the RNA-binding protein Unkempt at its effector interface.Nature communications · 2024Article
- Eukaryotic initiation factor 5A hypusine as a negative regulator of adenosine 2B receptor (A2bAR) through interaction with stem loop sequences within the A2bAR 3'-untranslated region.Molecular biology reports · 2023Article
- PRIESSTESS: interpretable, high-performing models of the sequence and structure preferences of RNA-binding proteins.Nucleic acids research · 2022Article
- High-throughput techniques enable advances in the roles of DNA and RNA secondary structures in transcriptional and post-transcriptional gene regulation.Genome biology · 2022Review
- Theoretical studies on RNA recognition by Musashi 1 RNA-binding protein.Scientific reports · 2022Article
- RNANetMotif: Identifying sequence-structure RNA network motifs in RNA-protein binding sites.PLoS computational biology · 2022Article
- PhyloPGM: boosting regulatory function prediction accuracy using evolutionary information.Bioinformatics (Oxford, England) · 2022Article
- Secondary structure prediction for RNA sequences including NNature communications · 2022Article
- Coupling axonal mRNA transport and local translation to organelle maintenance and function.Current opinion in cell biology · 2022Review
- The disease-associated proteins Drosophila Nab2 and Ataxin-2 interact with shared RNAs and coregulate neuronal morphology.Genetics · 2022Article
- Neuronal Cells Display Distinct Stability Controls of Alternative Polyadenylation mRNA Isoforms, Long Non-Coding RNAs, and Mitochondrial RNAs.Frontiers in genetics · 2022Article
55 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
While many RNA-binding proteins (RBPs) bind RNA in a sequence-specific manner, their sequence preferences alone do not distinguish known target RNAs from other potential targets that are coexpressed and contain the same sequence motifs. Recently, the mRNA targets of dozens of RNA-binding proteins have been identified, facilitating a systematic study of the features of target transcripts. Using these data, we demonstrate that calculating the predicted structural accessibility of a putative RBP binding site allows one to significantly improve the accuracy of predicting in vivo binding for the majority of sequence-specific RBPs. In our new in silico approach, accessibility is predicted based solely on the mRNA sequence without consideration of the locations of bound trans-factors; as such, our results suggest a greater than previously anticipated role for intrinsic mRNA secondary structure in determining RBP binding target preference. Target site accessibility aids in predicting target transcripts and the binding sites for RBPs with a range of RNA-binding domains and subcellular functions. Based on this work, we introduce a new motif-finding algorithm that identifies accessible sequence-specific RBP motifs from in vivo binding data.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.